How to filter for evalue threshold in blastx output
I used blastx to search DNA fasta files for proteins that I compiled to a costum database using makeblastdb -dbtype prot. The blastx command I used is as follows:
blastx -query sample1.fasta -db costum_DB -out result_sample1.tsv -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore" -num_threads 12
Then I used the following command to print the number of hits of each protein in my input fasta file.
cut -f2 result_sample1.tsv | sort | uniq -c > summy_of_hits_sample1.tsv
My question is: how can I filter or print only hits with a minimum e-value? The maximum e-value given now is 10 and I want to only count hits where the e-value is 0.01. Since the e-value is present in column 11, I guess there might be a possibility to filter?
• 1,456 views
•
link
2 answers
-evalue 0.01
and
-outfmt 6
The std output for format 6 is the same you specified, no need to specify it twice
• 0 views
•
link
Log in to answer this question.